select

Select simulation data from SimData object using expressions

Syntax

[t,x,names] = select(simdata,query)

sdOut = select(simdata,query)

___ = select(simdata,query,'Format',formatValue)

Description

[t,x,names] = select(simdata,query) returns the simulation time points t, the simulation data x, and corresponding names for the data columns that match query.

sdOut = select(simdata,query) returns the simulation results that match the query as a SimData object sdOut.

___ = select(simdata,query,'Format',formatValue) returns the queried simulation data in the specified data format.

Examples

Select Simulation Data Using Names and Regular Expressions

Load the model of glucose-insulin response. For details about the model, see the Background section in Simulating the Glucose-Insulin Response.

sbioloadproject('insulindemo.sbproj','m1');

Suppress an information warning that is issued during simulations.

warnSettings = warning('off', 'SimBiology:DimAnalysisNotDone_MatlabFcn_Dimensionless');

Simulate a single meal for a normal subject for 7 hours.

singleMeal = sbioselect(m1,'Name','Single Meal');
cs = getconfigset(m1,'active');
cs.StopTime = 7;
sd = sbiosimulate(m1,singleMeal)

 
   SimBiology Simulation Data
 
   ModelName:        Cobelli's Glucose-Insulin System
   Logged Data:
     Species:        15
     Compartment:    0
     Parameter:      24
     Sensitivity:    0
     Observable:     0
 

sbioplot(sd);

Select all species data logged in the SimData object sd.

[t,x,names] = select(sd,{'Type','species'});
names

names = 15x1 cell
    {'Glucose appearance.Dose'              }
    {'Glucose appearance.Stomach Glu Solid' }
    {'Glucose appearance.Stomach Glu Tritur'}
    {'Glucose appearance.Stomach Glu'       }
    {'Glucose appearance.Gut Glu'           }
    {'Glucose appearance.Plasma Glu'        }
    {'Glucose appearance.Plasma Glu Conc'   }
    {'Glucose appearance.Tissue Glu'        }
    {'Insulin secretion.Interstitial Ins'   }
    {'Insulin secretion.Portal Ins'         }
    {'Insulin secretion.Liver Ins'          }
    {'Insulin secretion.Plasma Ins'         }
    {'Insulin secretion.Plasma Ins Conc'    }
    {'Insulin secretion.Ins Delay 1'        }
    {'Insulin secretion.Ins Delay 2'        }

Plot data for the glucose rate of appearance and glucose utilization, namely Glu Appear Rate and Glu Util.

newsd = select(sd,{'Type','parameter','name',{'Glu Appear Rate'; 'Glu Util'}})

 
   SimBiology Simulation Data
 
   ModelName:        Cobelli's Glucose-Insulin System
   Logged Data:
     Species:        0
     Compartment:    0
     Parameter:      2
     Sensitivity:    0
     Observable:     0
 

sbioplot(newsd);

Compare data for the plasma glucose concentration (the species named Plasma Glu Conc) and insulin secretion rate (the parameter named Ins Secr). Use selectbyname to extract data by specifying the corresponding names.

newsd2 = selectbyname(sd,{'Plasma Glu Conc','Ins Secr'})

 
   SimBiology Simulation Data
 
   ModelName:        Cobelli's Glucose-Insulin System
   Logged Data:
     Species:        1
     Compartment:    0
     Parameter:      1
     Sensitivity:    0
     Observable:     0
 

sbioplot(newsd2);

Select data for all species and parameters that have Glu in their names.

newsd3 = select(sd,{'Where','Name','regexp','Glu'})

 
   SimBiology Simulation Data
 
   ModelName:        Cobelli's Glucose-Insulin System
   Logged Data:
     Species:        7
     Compartment:    0
     Parameter:      11
     Sensitivity:    0
     Observable:     0
 

newsd3.DataNames

ans = 18x1 cell
    {'Stomach Glu Solid'       }
    {'Stomach Glu Tritur'      }
    {'Stomach Glu'             }
    {'Gut Glu'                 }
    {'Plasma Glu'              }
    {'Plasma Glu Conc'         }
    {'Tissue Glu'              }
    {'Stomach Glu After Dosing'}
    {'Glu Appear Rate'         }
    {'Glu Prod'                }
    {'Plasma Glu Conc Rate'    }
    {'Ins Dep Glu Util'        }
    {'Glu Util'                }
    {'Glu Excretion'           }
    {'Glu Excretion Mode'      }
    {'Delayed Glu Signal'      }
    {'Delayed Glu Signal Mode' }
    {'Basal Glu Prod'          }

You can also return the selected data as a structure.

sdStruct = select(sd,{'Where','Name','regexp','Glu'},'Format','struct');

Restore the warning settings.

warning(warnSettings);

Input Arguments

simdata — Simulation data

SimData object | array of SimData objects

Simulation data, specified as a SimData object or array of SimData objects.

query — Search query

cell array of character vectors | string vector

Search query, specified as a cell array of character vectors or a string vector. The query consists of some combination of name-value pair arguments or 'Where' clauses. For a more complete description of the query syntax, including 'Where' clauses and their supported condition types, see sbioselect. However, the only boolean operator that the function supports is and.

You can use any of the metadata fields available in the DataInfo property of a SimData object in the query. The fields include 'Type', 'Name', 'Units', 'Compartment' (for species only), and 'Reaction' (for parameters only).

Example: {'Type','species'}

Data Types: string | cell

formatValue — Simulation data format

character vector | string

Simulation data format, specified as a character vector or string. Some formats require you to specify only one output argument. The valid formats follow.

• 'num' — This format returns simulation time points and simulation data in numeric arrays and the names of quantities and sensitivities as a cell array. This format is the default when you run getdata with multiple output arguments.

• 'nummetadata' — This format returns a cell array of metadata structures instead of the names of quantities and sensitivities as the third output argument.

• 'numqualnames' — This format returns qualified names in the third output argument to resolve ambiguities.

You must specify only one output argument for the following formats.

• 'simdata' — This format returns data in a new SimData object or an array of SimData objects. This format is the default when you specify a single output argument.

• 'struct' — This format returns a structure or structure array that contains both data and metadata.

• 'ts' — This format returns data as a cell array.

  • If simdata is scalar, the cell array is an m-by-1 array, where each element is a timeseries object. m is the number of quantities and sensitivities logged during the simulation.

  • If simdata is not scalar, the cell array is k-by-1, where each element of the cell array is an m-by-1 cell array of timeseries objects. k is the size of simdata, and m is the number of quantities or sensitivities in each SimData object in simdata. In other words, the function returns an individual time series for each state or column and for each SimData object in simdata.

• 'tslumped' — This format returns the data as a cell array of timeseries objects, combining data from each SimData object into a single time series.

Output Arguments

t — Simulation time points

numeric vector | cell array

Simulation time points, returned as a numeric vector or cell array. If simdata is scalar, t is an n-by-1 vector, where n is the number of time points. If simdata is an array of objects, t is a k-by-1 cell array, where k is the size of simdata.

x — Simulation data

numeric matrix | cell array

Simulation data, returned as a numeric matrix or cell array. If simdata is scalar, x is an n-by-m matrix, where n is the number of time points and m is the number of quantities and sensitivities logged during the simulation. If simdata is an array of objects, x is a k-by-1 cell array, where k is the size of simdata.

names — Names of quantities and sensitivities

cell array

Names of quantities and sensitivities logged during the simulation, returned as a cell array. If simdata is scalar, names is an m-by-1 cell array. If simdata is an array of objects, names is a k-by-1 cell array, where k is the size of simdata.

sdOut — Simulation results

SimData object

Simulation results, returned as a SimData object.